Roland, I'm not quite sure that I follow exactly what you are proposing, but you may be interested in our recent preprint on handling inapplicable data: https://www.biorxiv.org/content/early/2017/10/26/209775
This solution to inapplicable data is implemented in the R package TreeSearch. I'm still working on making this package easier to use so would be interested to hear whether you find it useful. Cheers, Martin -- *Martin R. Smith* Assistant Professor in Palaeontology Department of Earth Sciences Durham University Mountjoy Site, South Road Durham DH1 3LE *T*: +44 191 334 2320 *M*: +44 774 353 7510 *E*: martin.sm...@durham.ac.uk *Skype*: martin--smith durham.ac.uk/earth.sciences/staff/academic/?id=14260 twitter.com/PalaeoSmith The information in this e-mail and any attachments is confidential. It is intended solely for the addressee or addressees. If you are not the intended recipient please delete the message and any attachments and notify the sender of mis-delivery. Any use or disclosure of the contents of either is unauthorised and may be unlawful. Although steps have been taken to ensure that this e-mail and any attachments are free from any virus, we advise the recipient to ensure they are indeed virus free. All liability for viruses is excluded to the fullest extent permitted by law. > Message: 1 > Date: Thu, 8 Feb 2018 17:27:54 +0100 > From: Roland Sookias <r.sook...@gmail.com> > To: r-sig-phylo@r-project.org > Subject: [R-sig-phylo] Not inferring homology within "absence" state > in phylogenetic analysis > Message-ID: > <CA+PBJbmF2-_VE=4HuXZ610kh_Dtm2i4hK7CZkcfza2yN=1UrOg@ > mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all > > Maybe someone has some insight here... > > I am coming up against the problem, when it comes to phylogenetic analysis. > Basically I want to conduct a parsimony (or other phylogenetic) analysis > where "inapplicable" scores are treated as separate states *for each taxon* > . > > I.e. I want to hypothesize shared ancestry for taxa scored with one state > (let's say state 0), but not hypothesize shared ancestry for the other > taxa. However, I still want to penalize a change in state from and to state > 0. > > There are three approaches which I have thought about, but none seems to > fit the bill: > > -Score all taxa not showing state 0 as separate states. This should do what > I want, but the problem here is the limit on the number of states in most > programmes. > > -Scoring binary presence/absence. The problem is here that it could end up > being parsimonious to group the "absence" state together, when there is no > reason to infer homology within (i.e. for taxa scored with) this state. > > -Score as 0 and inapplicable. The problem is this does not penalize a > change from 0 to inapplicable. > > A real life example, is the shape of the ilium in crocodiles. I want to say > that it is likely that a particular curve in the dorsal margin of the ilium > in crocodile-line crocodilians is homologous, but I don't want to > hypothesize homology of those taxa "lacking" this state. They are all > equally far from each other. > > Thanks very much indeed > > Best > > Roland Sookias > > [[alternative HTML version deleted]] > > > > [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/